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- PDB-7eny: Crystal structure of hydroxysteroid dehydrogenase from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 7eny
TitleCrystal structure of hydroxysteroid dehydrogenase from Escherichia coli
Components7alpha-hydroxysteroid dehydrogenase
KeywordsHYDROLASE / ketolithocholic acid / alcohol dehydrogenase / hydroxysteroid dehydrogenase / ursodeoxycholic acid
Function / homology
Function and homology information


chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / 7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase activity / bile acid catabolic process / lipid catabolic process / NAD binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
7alpha-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsKim, K.-H. / Lee, C.W. / Pardhe, D.P. / Hwang, J. / Do, H. / Lee, Y.M. / Lee, J.H. / Oh, T.-J.
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2021
Title: Crystal structure of an apo 7 alpha-hydroxysteroid dehydrogenase reveals key structural changes induced by substrate and co-factor binding.
Authors: Kim, K.H. / Lee, C.W. / Pardhe, B.D. / Hwang, J. / Do, H. / Lee, Y.M. / Lee, J.H. / Oh, T.J.
History
DepositionApr 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7alpha-hydroxysteroid dehydrogenase
B: 7alpha-hydroxysteroid dehydrogenase
C: 7alpha-hydroxysteroid dehydrogenase
D: 7alpha-hydroxysteroid dehydrogenase
E: 7alpha-hydroxysteroid dehydrogenase
F: 7alpha-hydroxysteroid dehydrogenase
G: 7alpha-hydroxysteroid dehydrogenase
H: 7alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)242,5648
Polymers242,5648
Non-polymers00
Water2,648147
1
A: 7alpha-hydroxysteroid dehydrogenase
B: 7alpha-hydroxysteroid dehydrogenase
C: 7alpha-hydroxysteroid dehydrogenase
D: 7alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)121,2824
Polymers121,2824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-90 kcal/mol
Surface area35500 Å2
MethodPISA
2
E: 7alpha-hydroxysteroid dehydrogenase
F: 7alpha-hydroxysteroid dehydrogenase
G: 7alpha-hydroxysteroid dehydrogenase
H: 7alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)121,2824
Polymers121,2824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-94 kcal/mol
Surface area35970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.829, 100.188, 160.219
Angle α, β, γ (deg.)90.000, 95.571, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
7alpha-hydroxysteroid dehydrogenase / 7alpha-HSDH / NAD-dependent 7alpha-hydroxysteroid dehydrogenase


Mass: 30320.455 Da / Num. of mol.: 8 / Mutation: F2L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: hdhA, hsdH, b1619, JW1611 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0AET8, 7alpha-hydroxysteroid dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.62 %
Crystal growTemperature: 294 K / Method: evaporation
Details: 0.1 M HEPES:NaOH pH 7.5, 20% (w/v) PEG 4000, and 10% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 50045 / % possible obs: 98.7 % / Redundancy: 3.6 % / CC1/2: 0.98 / Net I/σ(I): 16.7
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 2487 / CC1/2: 0.776

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FMC

1fmc


Resolution: 2.703→38.093 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.878 / SU B: 17.603 / SU ML: 0.355 / Cross valid method: FREE R-VALUE / ESU R Free: 0.448
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.293 2490 4.982 %
Rwork0.198 47490 -
all0.203 --
obs-49980 98.306 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 58.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.028 Å20 Å2-0.014 Å2
2--0.019 Å20 Å2
3---0.012 Å2
Refinement stepCycle: LAST / Resolution: 2.703→38.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14381 0 0 147 14528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01314594
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714207
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.62119747
X-RAY DIFFRACTIONr_angle_other_deg1.2311.57732638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.26951952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.91423.948651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.059152433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2721565
X-RAY DIFFRACTIONr_chiral_restr0.0630.22031
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216939
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023171
X-RAY DIFFRACTIONr_nbd_refined0.2130.23198
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.214143
X-RAY DIFFRACTIONr_nbtor_refined0.1540.26992
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.27466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2403
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0710.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.229
X-RAY DIFFRACTIONr_nbd_other0.1710.2117
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2330.25
X-RAY DIFFRACTIONr_mcbond_it4.9996.1057847
X-RAY DIFFRACTIONr_mcbond_other4.996.1057846
X-RAY DIFFRACTIONr_mcangle_it7.5639.1369783
X-RAY DIFFRACTIONr_mcangle_other7.5629.1369784
X-RAY DIFFRACTIONr_scbond_it4.9286.5656747
X-RAY DIFFRACTIONr_scbond_other4.9286.5666748
X-RAY DIFFRACTIONr_scangle_it7.5899.6589963
X-RAY DIFFRACTIONr_scangle_other7.5889.6599964
X-RAY DIFFRACTIONr_lrange_it10.91673.25715565
X-RAY DIFFRACTIONr_lrange_other10.91573.26315566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.703-2.7730.3551680.2493402X-RAY DIFFRACTION96.1487
2.773-2.8490.3361660.2353481X-RAY DIFFRACTION100
2.849-2.9320.3241770.2273380X-RAY DIFFRACTION99.9719
2.932-3.0220.3441630.2143259X-RAY DIFFRACTION99.8832
3.022-3.1210.3141620.2233182X-RAY DIFFRACTION99.9402
3.121-3.230.3411610.2143074X-RAY DIFFRACTION100
3.23-3.3520.3511490.222934X-RAY DIFFRACTION99.8704
3.352-3.4890.3161360.2012892X-RAY DIFFRACTION99.7037
3.489-3.6440.2841340.1732739X-RAY DIFFRACTION99.6531
3.644-3.8220.2731320.1792607X-RAY DIFFRACTION99.5276
3.822-4.0290.2621450.1842469X-RAY DIFFRACTION99.3539
4.029-4.2730.2581300.1612321X-RAY DIFFRACTION98.7908
4.273-4.5680.2661090.1542170X-RAY DIFFRACTION97.1027
4.568-4.9330.2791290.1721987X-RAY DIFFRACTION96.8421
4.933-5.4040.2731030.21841X-RAY DIFFRACTION97.4925
5.404-6.0410.281050.1911688X-RAY DIFFRACTION98.5165
6.041-6.9730.288810.1711518X-RAY DIFFRACTION98.948
6.973-8.5370.247720.191231X-RAY DIFFRACTION94.9017
8.537-12.0550.283370.246830X-RAY DIFFRACTION80.6512
12.055-30.0930.375310.318483X-RAY DIFFRACTION83.9869

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